Contacts of the strand formed by residues 169 - 176 (chain E) in PDB entry 5LK5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 169 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E THR* 3.6 34.1 - - + +
97E VAL 3.6 6.5 - - - +
98E LYS* 3.3 17.5 - - + +
168E PHE* 1.3 72.3 - - - +
170E HIS* 1.3 68.3 + - - +
329E ASN* 5.9 0.9 - - - +
347E TRP* 3.3 25.5 + - + -
350E THR* 4.0 18.7 - - + +
351E LYS* 6.0 1.1 - - - -
354E GLU* 2.5 38.0 + - - +
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Residues in contact with HIS 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E THR* 3.3 4.1 - - - -
97E VAL 2.8 38.7 + - - +
164E LYS* 3.4 38.2 - - + +
166E ASP* 2.7 34.8 + - - -
168E PHE* 3.4 27.3 + - + -
169E THR* 1.3 80.2 + - - +
171E LEU* 1.3 61.2 + - - +
172E TYR* 3.8 23.2 - - + -
186E ILE* 4.7 1.3 - - + -
187E ASP* 2.8 28.1 + - - +
347E TRP* 4.4 2.9 + - - -
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Residues in contact with LEU 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN* 3.6 34.3 - - + +
95E PHE 3.7 6.5 - - - +
96E THR* 3.8 20.4 - - + -
170E HIS* 1.3 70.9 - - - +
172E TYR* 1.3 60.1 + - - +
173E THR* 4.1 8.3 - - - +
185E LYS 3.7 0.2 - - - +
186E ILE* 3.2 10.2 - - - +
187E ASP* 2.8 38.8 + - - -
188E ASN* 3.8 32.8 - - + +
329E ASN 5.4 1.6 - - - +
343E GLY* 3.8 25.8 - - - -
346E THR* 4.8 2.9 - - - +
347E TRP* 3.9 23.4 - - + -
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Residues in contact with TYR 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E VAL 3.8 0.2 - - - +
94E GLN* 3.2 5.9 - - - +
95E PHE* 2.9 43.2 + - + +
97E VAL* 4.1 14.6 - - + -
132E PHE* 3.8 17.6 - + + -
134E PRO* 3.7 36.3 - - + +
144E VAL* 3.9 24.0 - - + -
163E CYS* 3.5 5.2 - - - +
164E LYS* 3.0 35.0 + - - +
170E HIS* 3.8 27.1 - - + -
171E LEU* 1.3 71.4 - - - +
173E THR* 1.3 62.3 + - - +
184E VAL* 5.8 0.2 - - + -
185E LYS 3.6 2.7 - - - -
186E ILE* 3.8 35.0 - - + -
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Residues in contact with THR 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E VAL* 3.8 23.1 - - + -
93E VAL 3.4 3.6 - - - +
94E GLN* 2.8 30.1 + - - +
132E PHE* 3.5 7.8 - - - -
171E LEU* 4.1 10.0 - - - +
172E TYR* 1.3 76.0 - - - +
174E LEU* 1.3 60.8 + - - +
175E ILE* 4.2 13.7 - - + -
183E GLU 3.9 0.5 - - - +
184E VAL* 3.4 5.5 - - - -
185E LYS* 2.9 58.9 + - + +
188E ASN* 4.7 2.2 + - - +
339E ALA* 4.8 2.5 - - + -
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Residues in contact with LEU 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E LEU 3.7 1.0 - - - +
92E VAL* 3.3 6.8 - - - +
93E VAL* 2.8 46.0 + - + +
130E ILE* 4.1 26.0 - - + -
132E PHE* 3.5 32.5 - - + -
146E VAL* 3.9 25.4 - - + -
148E PHE* 5.2 1.6 - - + -
173E THR* 1.3 74.0 - - - +
175E ILE* 1.3 71.9 + - - +
176E VAL* 4.0 21.8 - - + -
182E TYR* 4.6 6.7 - - + -
183E GLU 3.7 9.0 - - - +
184E VAL* 4.0 12.6 - - + -
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Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E THR* 4.0 11.4 - - + -
91E LEU 3.5 2.5 - - - +
92E VAL* 4.2 8.1 - - + -
173E THR* 4.2 12.6 - - + -
174E LEU* 1.3 75.2 - - - +
176E VAL* 1.3 64.7 + - - +
177E ARG* 4.1 14.4 - - + +
182E TYR* 3.0 9.6 - - - +
183E GLU* 2.9 50.7 + - + +
185E LYS* 4.4 28.0 - - + +
336E GLU* 3.6 52.9 - - + +
339E ALA* 6.1 0.4 - - + -
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Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASN* 4.8 3.3 + - - +
89E GLN 4.0 1.6 - - - +
90E THR* 3.4 3.0 - - - +
91E LEU* 2.8 51.4 + - + +
130E ILE* 5.0 5.6 - - + -
148E PHE* 3.8 30.1 - - + -
174E LEU* 4.0 22.9 - - + -
175E ILE* 1.3 79.4 - - - +
177E ARG* 1.3 65.1 + - - +
181E THR 3.8 5.2 - - - +
182E TYR* 4.5 2.9 - - + +
196E LEU* 4.8 4.5 - - + -
306E TYR* 3.8 37.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il